Penance
by Ms. Unusual-in-Groovy-Ways
Summary: Why does a good man go to war? Why would he risk his life to save those who never get a chance to say "thank you"? What happened all those years ago that keeps him running? Questions are answered and the 11th Doctor must face his childhood, the Last Great Time War, and his most haunting memory...his first wife.
1. I: The Aftermath is Secondary

**A/N/: **Greetings my fellow Whovians (I love this word)! In case you didn't see, I'm Ms. Unusual-in-Groovy-Ways and I welcome you to my very first Doctor Who fanfic! I usually write X-Men and Glee stuff, but I've been recently watching the Doctor on Netflix and, needless to say, I was inspired. As a fair warning, I'm notoriously slow at updating because I do so while I am interested, but, when I move on to another idea, I forget about my stories. (Which explains my 7 pending fanfics.)

All right, I'm babbling like 10, so let's move on! As you may know, this story is about the Doctor finding out that someone from his past is actually alive - I'm not telling you who, though. Despite the fact that I only finished series 2 days ago (emotionally shocked, people), I'm writing about 11. This is preferably non-canon so Rory and Amy are still here. Got that?

O.K., lastly, please read and review! I adore feedback - especially for stories that are my first in a fandom. And because I haven't met the Eleventh Doctor yet, please tell me when my personally traits stray from the real thing, 'kay?

I'm talking too much again, so bid thee good byes!

~Ms. Unusual-in-Groovy-Ways

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**DISCLAIMER: I do NOT own Doctor Who or any references to the show or anything else. 'Cause if I did, I'd be killing more people off than Moffat.**

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_**Penance**_

_**I**_

_**The Aftermath is Secondary**_

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Their voices croak out orders all around her, surrounding her in a sphere of barking frustration. They yell and command, but she can tell nothing is being accomplished. The leader's voice is the deepest and as it orders his subjects to obey, she can feel his vibrations rattle her spine in absolute terror. His voice creeps up and down whatever holding area she is in, bringing back the suppressed memories of her far away youth.

She can remember the dark rooms of the war prisons. Merely medium-to-large metal cages that they were forced into, like dogs. They would throw prisoners in there, in the black dark, and make them just sit there, simply. But it was not so simple as _just_ sitting there. It was the lack of food and the howling of the dying wounded that was torture. You would hear the calling, the pleading of your fellow soldiers - sometimes civilians, like her - for their loved ones. Or, when they were feeling "generous" they would put families in the same holding chamber, making them scream for wives, husbands from across the corridor- anyone to quench the thrist of death they all craved in that black-hole of a war ship.

The immensely disturbing memories flooded her head as the leader commanded more soldiers to go to the landing area in level 5. She heard them comfirm and then fly off to the destination, knowing that her friends were doomed at best if they continued to be outnumbered. But as she kneeled on bloodied knees, blind-folded and chained, in front of the King Dalek, she had a flicker of faith that Amy, Rory, and her Doctor would come for her, as he had promised all those years ago.

*Rhea was her name, the name of our prisoner. She was taken three days ago from the TARDIS in the middle of the night in surprise raid. She had not seen a Dalek in years, or so she thought. They had stunned her, leaving paralyzed as she bared to hear the sound of Amelia Pond's frantic screaming or Rory hysterically yelling his wife's name or the Doctor, whose voice roared louder than any gun shot she had ever witnessed, begging the Daleks over and over again "to leave them alone".

Rhea fainted as running footsteps came towards her room. She awoke dazed two days later in this very spot, bound and blinded, hearing only the sounds of the Daleks, wo were always calling out orders to kill.

Now she knew that her friends were in level 5, fighting off hordes of enemies, only to rescue them. The second-in-command kept the King informed. She'd overheard that none of them were injured, that they were coming in and out of the TARDIS for protection. However, she could not possibly believe their words until her friends, those three clowns, walk in, all cut and bruises, ready to take her home.

"Your Majesty," the second-in-command Dalek drawled, "the Doctor has escaped capture. He is heading to the boarding area on level one hundred."

"What of the inferiors?" the King inquired in his hauntingly deep voice. It really frightened her when he spoke; it was no understatement. It sounded like a hum of an engine, smooth and low, but it cracked like lightning and barked like thunder. The ground rumbled when he talked.

"They have escaped in the TARDIS. They have fled."

Rhea's hearts failed to beat. Having her sight taken away, she relied heavily on her sense of sound to perceive her surroundings. From the noises around her and what her captors have said, she knew she was in boarding area level 100. This where only the most élite Daleks generals stayed and received the worst weapons. Her Doctor was now alone, merely equiped a screwdriver (for heaven's sake!), and was going to walk in and defeat all those villains?! Rhea had learned that the Doctor was the Messiah of worlds and had brought down threats with six simple words. But to single-handed destroy hundreds of furious, dangerous Daleks and come back alive? Rhea's faith fell as the lift's door blasted open.

She may not have seen him walk in, but the Dalek's frantic "EX-TER-MI-NATE!"s told her that the Doctor had arrived. But what she did not hear was the liquid fear in those funny robot voices, the pure, untouched fear in their trembling calls. She could not see that the Doctor was bloodied and battered, his clothes torn and smoking. She couldn't see the rapid rising and falling of his chest as he casually strutted toward the King. But what she did not see - or wanted to, nonetheless - was the murderous expression on his usually beautifully cheeky face. His eyes were lined with black-and-blue marks, their color so bright that the brown was drowned with red. His bleeding lips could not even cover the hateful sneer his mouth made. But what Rhea never, ever, ever saw coming was the small, silver gun in his hand...

...Or the fact that as he came closer, he shot a tiny but fatal bullet through the back of her head.

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* _Rhea (pronounced **REE-ah**), _Greek goddess of the earth, mother of the Olympians, and wife of Chronos


	2. II: Calm Before the Storm

**A/N: **Please note this chapter has been edited from its original draft due to difficulty with furthering the plot. Also, the name of this story, the chapters' titles, and the summary have been edited. I hope this does not cause any complications.

~Ms. Unusual-in-Groovy-Ways

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**DISCLAIMER: I do NOT own _Doctor Who_ or any references to the show or anything else for that matter. 'Cause if I did, I'd be killing more people off than Moffat. ;)**

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_**Penance**_

_**II**_

_**Calm Before the Storm**_

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**(six months prior)**

It was an ordinary day for the Doctor and his current companions, Rory Williams and Amy Pond - if drifting off into a foreign time, discovering something supernatural or extraterrestrial, saving the world, and possibly having your friends _think_ that you _died_ in the process is what you call "ordinary". If so, then the Doctor and his married pair have had a completely mundane afternoon, merely saving Barcelona (the planet) from giant, radioactive flesh-eating spiders.

The trio sluggishly carried themselves onto the TARDIS. They all collapsed from exhaustion with dull thuds, enjoying the horribly filthy yet surprising comfy ground.

"I want to die," Amy announced in monotone.

"Don't...don't say that," Rory barely countered. He was so tired from being partially fed to those spiders, he couldn't muster enough strength to form a coherent sentence.

Suddenly, as if their day was nonexistent, the Doctor popped up from behind the controls with a frighteningly happy smile on his face.

"What is this?" he asked rhetorically. "How come your just laying there? Get up! There's no time for laziness! We have a movie to catch, you know? I always prefer to be early when seeing the first _Star Wars_ film."

Amy propped herself up on her elbows, her legs lying limply in front of her. "Doctor, we've just came back! How can we see a film like this?"

The Doctor cocked his head to the side curiously. "'Like this?' Well, I'd think that since you travel 'round with an alien in a time-traveling spaceship you'd be more up for a sci-fi film. But if that's the case -"

"No, no, no, Doctor!" Amy stood up slowly and made her toward her simple friend. "What I mean is - we just got back - literally! How can we go back to 1999 when Rory and I haven't had a minute of proper rest?"

The Doctor looked at her like a rebuked child. "I-I said the 'first _Star Wars_ film,' so it's actually 1977, technically."

Amy let out a frustrated sigh. She put on her best "mom" face and pointed a finger at the Doctor. "Now you listen here, young man. Rory almost died..._again_! Haven't you been keeping track? We have not been inside the TARDIS five minutes and you already want to challenge Darth Vader to a-a-a cook-off, for all we know! And why haven't we just gone out for a walk? Go to the park and have a picnic? If we're a family, let's go to a _normal movie_, like _normal_ people. Let's have a proper sit-down dinner, with actual food - not that mystery meat that has been in this ship since 1842 or whatever! I'm not forcing my husband to battle alien...kittens just so you can see a movie you've seen five thousand times!"

The Doctor hung his dead sadly. "Fine. We'll wait 'til tomorrow then," he muttered quietly.

Amy rolled her eyes. "That's not what I'm saying, Doctor! I want to have a normal day...Didn't you have any when you were little? Or your parents were too Time Lord for that?"

The Doctor's eyes quickly flashed with anger. He stared at Amy like she had called him, his mother, and the horse she'd rode in on trout-faced hags.

"It is _my_ TARDIS. I go where I_ want_ to. You and Rory are guests. If you don't want to go, stay in your rooms."

"Oi," Rory spoke up as he collected himself to stand straight "You don't have to be rude about. Amy's just a bit cranky, that's all."

"No, I'm not! He's just not human enough to understand -."

"STOP IT!" the Doctor yelled. His chest was heaving rapidly and his hands were curled into fists. As he spoke painfully, he clamped his eyes shut and talked with his hands, never unclenching them. "I'm more human than you and your mortal brain will ever comprehend. Never - _ever!_ - speak to me like I'm a naÏve...child with problems. I'm as normal as I get and if you don't like it, I'm so sorry."

He stormed off, next, not looking back to show them the silent tears that are erupting. That comment Amy unconsciously said about his parents had really unsettled him. He didn't think about them often but as she talked of picnics and parks and real dinners he thought of memories to hurtful to think. Things Amy and Rory would never truly understand. Because they _were too_ Time Lord for them. They wouldn't understand the unconventional emotions that come with being Gallifreyan.

So as he sat there in his room, quietly tearing up, a loud _ZAP!_ broke his reverie. He stood up then, rolling his eyes at the idea of leaving a cranky maybe hungry Amy alone with the TARDIS controls with Rory, the unhappy Happy Meal.

As walked back to the source of the odd sound, the Doctor parted his lips to ask what the noise was, what he saw left him flabbergasted.

Being over one thousand years old, almost nothing scared nor surprised the wise, ancient Doctor. Maybe for a moment, but he possessed knowledge beyond his years, so puzzles were standard, everyday occurences. No need for _real_ alarm. But he looked straight at her and his hearts fall painfully slow into a black abyss called his stomach. The past cannot change, something he knew all too well, but as he made his way there, he knew it was her - no matter how impossible.

In the far corner of the room, next to doors, a shining white light blinded the trio. It eventually subsided to shimmering crouching figure of orange, gold, and silver. When that image left, the lights had left a girl - a small, shivering girl clad a tattered white dress that looked like it came from a _Pride & Prejudice_ adaptation. She sat with her knees close to chest and she had her battered arms wrapped around her body protectively. Her matted brown hair kept the time travelers from seeing her face.

Rory and the Doctor stayed in their respective places, not moving but gawking silently at their new guest. Amy, however, lost whatever edge she felt earlier and approached the girl. She walked to her slowly, not wanting to scare her. Then she sat in front of her and tried to brush her hair out of her face as she coaxed,

"Hello. I'm Amy Pond. No. No, don't worry," she added as the girl began to squirm. "I'm a friend. We all are. Are you okay? Do you need help?"

The mystery guest then lifted her head slightly so Amy could see her startling hazel eyes. They were spectacular, really. For a disheveled girl who looked like she went through and back, her eyes sparkled with majestic beauty and wise age.

The girl licked her lips before she spoke, like she was deathly nervous. She would not look Amy in the eyes as she spoke either. In fact, her eyes wandered around aimlessly, as if they searched for something specific in this strange place.

Amy's problem was not the girl's lack of confidence, but her lack of language. She muttered quietly, but in another language _entirely_. It sounded like Latin, or maybe Greek, with those nasally sounds of French added. But it also sounded like she was repeating the same gibberish again and again - aimlessly, like her eyes. Amy tried to keep her composure, to keep the girl calm, but she was confused and breaking the façade fast. How was she supposed to help her when she could not understand her? Did she understand Amy? Or was she freaking out in her language?

Amy held out her hands and the girl took them tightly. For the first time, the ragged guest gave a small smile of gratitude. Amy beamed back, but looked behind her, to the Doctor. Amy could act the part of a mother-figure for a while, but she someone to understand the girl, if not comforting would eventually prove to be fruitless.

The Doctor sighed and ran a hand through his hair. He walked towards the pair and kneeled. Looking down, away from those hazel orbs, he spoke in that odd dialect.

The girl's eyes flashed in fear in the Doctor's direction. Amy turned to him, silently asking him what he said. But as the Doctor began to speak, the girl started to scream into knees. She rocked back and forth violently, shaking her head. She cried to herself in a hurried voice, murmuring the same nonsense to herself over and over.

The Doctor's face contorted into a grimace. Like it hurt immensely to do it, he broke the sonic screwdriver and lifted the girl's face up. She started to breathe heavily, but the Doctor never lost a beat. He pulsed the sonic screwdriver into eyes and soon, her head flopped backward. She was unconscious.

Rory manned up and walked tentatively toward his wife and friend. He softly asked, "Doctor, no mean to be rude, who is this girl? Where is she from?"

The Doctor finally turned his attention to his companions. He sighed and with melancholy eyes, he barely whispered four simple words.

"This is my wife."


	3. III: Ambulance

**A/N/: **In case you didn't see the warning in chapter 2, the last chapter was edited from its original draft to a different version because I wasn't happy with the outcome. That, this story's name, the chapters' titles, and the summary have been changed too because I rushed my usual process to get this out and I didn't like how...unbeknownst everything was...if that makes sense. No that's all for now.

~Ms. Unusual-in-Groovy-Ways

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**DISCLAIMER: I do NOT own Doctor Who or any references to the show or anything else. 'Cause if I did, I'd be killing more people off than Moffat.**

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_**Penance**_

_**III**_

_**Ambulance**_

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In all honesty, that statement received "mixed reactions". Amy stood up slowly and walked toward the center of the TARDIS. She ran her hands through her hair before turning towards the Doctor, her arms crossed and her foot tapping. She wanted a fast explanation. Now.

Rory, on the other hand, quickly looked from the shriveled up girl to the Doctor several times, like he was watching a tennis match. After gawking for answers did not work, Rory fell limp like a rag doll, landing with a thud onto the dusty spaceship floor.

The Doctor heaved himself up and looked down at the girl he just knocked out. He then asked Amy, without looking away, "Amy, can you get the first aid kit from the stoage cupboard in the hall?"

"Oh no, sir!" she answered as strutted back to him. "I want answers first."

"Amy, not now. She is in critical condition. And it's obvious that the TARDIS is malfunctioning because of -"

Amy stood in front of the girl protectively. "You do not touch her until I get some talking out of you. Now speak."

"She needs medical attention. She's hurt and scared and I only partially knocked her out. She can hear all that's going on and I must treat before she flies off the handle again. Now move."

"Name."

"What?"

"What's her name?"

The Doctor sighed in frustration. "Just move please. Before she remembers that I -"

"What is her name?" Amy said, emphasizing every word.

"Amy, stop being so childish!" he grunted. "She needs help. Go get the kit."

"Why are you so freaked out? If she's your 'wife,' then she won't go on killing sprees."

"She's not my wife."

"That's not what you said a second ago."

The Doctor cursed under his breath and stomped toward the storage cupboard himself. Amy chased after him, still egging him on about the mystery girl's name. The Doctor kept quiet, although his anger was getting harder to hide. He got the first aid kit and raced back to the entrance. He approached the girl and gently lifted her up.

She looked so sad in his arms, Amy thought as she shut up. She was so frail and tiny, like a malnourished child. As the Doctor carried her into the light and away from the dark corner, Amy could really see the abuse she went through. Her dress was covered in dried blood and her ankles and wrists had broken gold-and-silver cuffs, their chains dangling heavily. She had bruises all over her and cuts and stitches from head to toe. On her right forearm, they were these odd scars that looked like tally marks. They were maybe ten or eleven cuts, some of them white scars and other still healing because of their newness.

"Just stand there," the Doctor said as he walked into the hallway. "Go open the door to my room. Then, please go and find something something suitable for her to wear. I hate to her so..." The Doctor never finished his sentence. His voice was thick with too much emotion.

Amy did as she was told, forgetting her own needs. She was about to run of to get some clean clothes, when the Doctor faintly whispered,

"Rhea. Her name is Rhea."


	4. IV: Fix (pt 1)

**A/N/: **All right. Listen. I love writing. I live to create. But I rely heavily on feedback. Yet,_ no one_ has reviewed! I only have one follower. I take that something is off about the story, but I won't know until I receive some comments. So please read and review!

~Ms. Unusual-in-Groovy-Ways

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**DISCLAIMER: I do NOT own Doctor Who or any references to the show or anything else. 'Cause if I did, I'd be killing more people off than Moffat.**

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_**Penance**_

_**IV**_

_**Fix (pt. 1)**_

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The TARDIS was a beautiful machine, Amy thought quietly as she sat nervously in front of the Doctor's bedroom door. Nothing in this universe was neither as marvelous nor unique. Literally one of kind she was.

Despite the simple exterior, the _bigger-on-the-inside_ technology of the Time Lords set the TARDIS out as a spaceship to be reckoned with. Also, the TARDIS was not any ol' ship. She was a living thing. She had a heart and a soul. Thoughts of her own, really. She was a caring creature who looked out for her owners, especially her Doctor.

The TARDIS had a mind of its own and her most amazing ability was the fact that she could change her interiors all by herself. Knowing her Time Lord well, she would construct and delete the rooms and spaces that he may or may not have needed. She had made a planetarium, a massive library, and even a fully stocked laboratory. But has companions came and went, the TARDIS changed drastically.

Hidden in the extensive walls of the infinite corridors, there was a room for every companion, each stocked with anything he/or she might have needed. For example, Rose Tyler needed a plushed out, girly room. Also, she was hungry girl, so the TARDIS made her a state-of-the-art kitchen.

Then there was Martha. She got homesick often, so there was a comfy, cozy living room. It was furished with huge, plush leather couches and real working fire place. The highlight of the room was the 72 in HD LCD 3D Ph.D falt screen TV with surround sound and a sick Blu-Ray DVD player with every movie known to mankind. (It was sick.)

Or Donna. The Doctor loved her to death, but she just a tad "high strung," if you know what I mean. So there was a tranquil garden, filled with canopies of tropical trees and exotic flowers. There was a water fall and koi pond. Or if it was a walk in the woods she wanted, there were firs and pines and moss-covered Redwoods. Not that Donna used or whatever, but it was a fabulous room.

Then there's Rory and Amy, the newest bunch on board. Rory was a sweet guy, but the Roman in him needed to be trained and primped, as the Doctor put it ("Romans don't get primped and pretty!"). So the TARDIS made him an all-out Colosseum. A miniature one, of course, but it was a glorious room. Any centurion would happily die for that space. Walls and hordes of weapons (ancient and modern). Dummies to practice on. Shooting ranges. Even robot animals to hunt and skin. ANd the place even had a TV, a pool table, and a mini-fridge, so Rory had a decked out mancave, basically.

Amy's place was less startling, but her own place all the same. She was an artsy kind of girl. Always humming a tune or doing a little jig. And she was a fantastic artist too. So the TARDIS made her an art studio/dance room/music room/spa (for good measure, the spa). Any art supply that would ever be needed was there. The mirrored walls and ballet handrails were professional at best. The music room had intruments as common as guitars, basses, and drums but even had alien ones like a Slitheen bomba or a rare Rocnoss hand flute.

The TARDIS was a handy gal. She knew her guests like her own children, the Doctor always said. So as Amy sat restlessly outside the door, the TARDIS automatically equiped the Doctor's room with everything he'd need to bring Rhea's health back. Amy hadn't been in yet, but she would have seen enough equipment to make Bones and Dr. Isles cry in jealousy. Scanners, tools, weird MRI machines and anything really that hospital needs to take care of their patients.

The door opened and Amy scrambled to get up. She looked at her Doctor longingly. He looked as raggedy as he had on that faithful day. His hair was tossled, his shirt scrunched up and unbuttoned in several places. He was sweaty and was bleeding from his hand.

"How...how is she?" Amy asked anxiously.

The Doctor slumped down against the wall opposite his room. Amy followed suit and examined his hand.

"She's terrible," he finally answered. "Just...*sigh*."

"What's the matter with her? Can it be helped?"

"I don't know. I don't know anything!" he muttered bitterly. "Her brain inaccessible. She couldn't be sedated or knocked-out. She squirmed at the slightest touch. She hates needles - don't get me started on that. She crumbles into a ball at the sight. Then when it came to telepathically look her over, her mind...so, so damaged. So..."

"_So_ what?"

"So _gone_, that's what! She has a parasite in her mind. A telepathic one. It's eating her brain, not physically of course. But her memories are...wasting away. Her personally is torn. It's breaking her head and she's desperately trying to fight it, but that's just making her worse. It's like fire, burning everything in its pass. Then that damn thing is undetectable so what use am I?!"

The Doctor kicked the wall in front him. Amy jumped in her seat. She had never heard the Doctor swear. I mean, he got upset and all, but Amy had always seen him as a gentleman, always composed even when he shouldn't have. He flew off, yeah, but never lowered himself to curse.

Amy changed the subject. "What was she saying earlier? The TARDIS never translated it."

"'Gods die. Gods bleed.'" he sighed. "It's an old Gallifreyan superstition. If you say in the darkest of times, it's supposed to ward off whatever demons are there. Ridiculous ritual, really. We'd abandoned it long ago. It was as backwards as the humans. No offense."

"Ummm...of course. So why she saying that?"

"Her head is dying. It feels groggy, clouded. Her head feels like it burning like hell. What would you do if you couldn't even articulate the pain you are in?"

"Oh," was Amy's reply. "Then how you do you know the exact pain? Did she tell you?"

"'A door once opened can be accessed from both sides.'"

Amy took that as a hint that the Doctor did not feel like talking anymore. She stood up. "Doctor, how about I stay and watch Rhea while you get some sleep? Even a Time Lord needs some time."

The Doctor stood up slowly, obviously in pain and tired. "Impossible. Whatever is in her head was meant to destroy her brain quickly, possibly by the time she came on board. Whoever did this wanted to make a statement. However, Huon particles are unruly. They should have known that. I need to work on restoring her mind enough so her subconscious can take over and eliminate the intruder."

"At least let me get her some clean clothes from the wardrobe."

"Already done."

"Doctor!" Amy's eyes grew large and shocked. She was surprised that the Doctor could take advantage of such a situation. The impropriety of it all...

"What?!" The Doctor threw in hands up in confusion, but then it hit him. "Oh, Amy! Really? Really?! Like I'd do something like that with her that way. The TARDIS did an automatic change! How highly do you think of me?"

"I'm sorry! But even after not seeing me for a day, I know how Rory gets..."

"Humans!" the Doctor yelled at the sky. "Everything's got to be in the gutter. Can never have a conversation without you beings giggling or blushing. I mean sheesh, just because I've of kissed every one of my companions, I'm instantly in love with them. I'd think after Rhea being here you'd understand why a snog is kind of nice _once_ in a while."

"How 'bout a shag?"

"Amelia Pond!"

"All right, all right!" Amy lifted her hands in surrender. She was smiling. "Just sayin', it's too early. No nurseries need to be popping up in the TARDIS just yet."


	5. V: Fix (pt 2)

**A/N: **Hello my fellow Whovians! Welcome back. I'm not going to write anything witty, so I'm sparing you. I just wanted to tell you that after this chapter (which is darker and longer than the last), the story will told through flashbacks, into the Doctor's past. The rest of the chapters will start at ground zero and build up to the current time and then the "six months later" part that I began with. Just wanted to warn you.

Also, I still insist that you guys review! Even if you're not subscribing or favorite-ing, leave a review to tell me why. Authors and artists strive for people to feedback info, so I'm not gonna be offended if the review is less than favorable. (Or, better, you can leave a raving review! :D)

T.G.I.F.,

~Ms. Unusual-in-Groovy-Ways

P.S. During the sadder parts of the chapter, I recommend listening to "To Beast or Not to Beast" from the_ X-Men: First Class_ soundtrack. It fits in quite nicely, actually.

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**DISCLAIMER: I do NOT own Doctor Who or any references to the show or anything else. 'Cause if I did, I'd be killing more people off than Moffat.**

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_**Penance**_

_**V**_

_**Fix (pt. 2)**_

* * *

The Doctor chuckled. He smiled to himself as Amy playfully ran away after their conversation took a turn for the...sexy, the Doctor guessed.

Oh, that was why the Doctor loved Amy. He thought happily of all the things she had done for him. Even the things he never noticed and didn't appreciate until now. Amy was the first companion not be infatuated with him. She was more like Donna that way. Neither stood there in awe and quietly followed whatever he said. They took action and said "no" when needed. But Donna, she still left the Doctor in his thoughts. She didn't like interfering. But Amy - she was not afraid to get in his business or pull out him of whatever Time Lord rage he possessed.

She took care of him. She's the first one to genuinely sit there and want to care for the man who did not think he could be cared for. When he needed someone to make him take something seriously, Amy was a reprimanding mother. When he was left secluded and lonely, she sat with him and let him babble on about the stars. He could be sad and Amy would hug him and give him a simple kiss on the cheek. Or like now. He was tired and upset, but he could not physically vocalize his actual frustration. Amy saw through that. She asked of his dying wife and empathized. Then when he shut down, she made him laugh.

That's what Amy does. She's sympathetic, a kind, loving person. But not a pushover. And the Doctor thanked those bright, shiny stars for Amy. He thanked them for giving him a girl that did not pale when compared to the other companions. She was her own self: cheeky, cranky, and all.

_Kind of like..._

_Stop it,_ the Doctor scolded. He could not think like that anymore. Rhea was back and he planned on keeping it that way. He should not think of _her_ and any the others in way that was...romantic, basically. And Amy - she was a friend. A _best_ friend. He needed to make sure that he never crossed that line, for the sake Rhea and Rory.

The Doctor paced around as he thought these things. He shook his head and slapped his face. He had seen human films that had done this, but he was disappointed that left feeling slightly worse. (His poor cheeks...)

* * *

After pepping himself up in the corridor, the Doctor reentered his _room-turned-intensive-care-unit_. His spirits feel immediately. As he walked farther into the room, the left side was lined with cabinets and shelves of medicines and tools. Big MRI and scanning machines were scattered around randomly. An X-ray machine sat beside the door. To the right was Rhea. She on a hospital bed, stirring in her restless sleep. A heart rate monitor was the sound beside her own occasional yells. On her left side, a transfusion stood high, supplying her with blood. The Doctor smirked as he remembered trying to stick that accursed needle into her arm. For a sickly little thing, she had major bite - literally.

The Doctor pulled up a chair and watched Rhea. He was so tired. Not from taking of her, no. She had been there for less than three hours. He could not allow himself to weaken with her being so fragile. But what led him to her arrival had exhausted any energy he had left out of him.

The Doctor never slept. He did not need it as much humans did. Plus, he had the most vivid nightmares. If it were not about his childhood - all distorted and exaggerated, of course, because it was through the eyes of a scared child - they were about the War. All those memories of death and carnage. What he saw his friends and family do. What he saw_ himself_ do for the sake king and country. He could never forgive himself for the things he'd done and if time was not so wibbly-wobbly, he would erase all he could. But time is complicated and delicate, so he has been forced to relive all those days.

Recently, the Doctor cannot help but sleep. He sometimes found himself unnaturally drowsy and dozing off during the worst times. It's so unusual! At first, they were about the Great War. The same reveries, the same chaos. Then they were about different parts of the War, not just Arcadia. The images were worse than he thought of they were. History of his neighbors' deaths, what his civilians had to go through - all played out. He'd wake up in sweat, just simply terrorized by what those filthy Daleks did. The dreams left him paranoid, but he could not let Rory or Amy see him so incapacitated.

Then the nightmares got even worse.

The Doctor tried not to think of Rhea - _ever_. It pained him too much to relive that day. Seeing her sacrifice herself for their...The Doctor couldn't. He just couldn't! He thought she died immediately, that the Daleks were merciful because she acted so gracefully heroic. But the night terrors said something else. She was held captive in those pitch black rooms, in a steel cage like animals. They hurt her constantly and then left her there to wallow. The dreams told him that that war ship left the star system before Gallifrey was burned to hell. But that didn't stop those Daleks. They continued to show no mercy to those Time Lords. In fact, it got worse. But an old Gallifreyan tradition* saved those innocent prisoners. They all died, in that's what you call humane. They died and didn't have to suffer anymore.

But Rhea wasn't so lucky. She was left there, alone, thinking she was the last Time Lady in existence. Then there was the fact she couldn't die. The Doctor always hated the scenes in his dreams where she sat there so sadly, crying. No one was touching her or hurting her, but her hearts ached so loudly. She missed her husband and their family and those skies and stars and home. She missed home so much.

And the Doctor felt so much for her as he witnessed those dreams. He felt so guilty too that he abandoned all hope so quickly. He did not check or search for her. He bitterly told himself that it was just him and his TARDIS - the last of the Gallifreyan race. But while he whined and cried, his wife was being tortured by Daleks and those filthy guards they hired.

Oh, those guards! The night before Rhea showed up the Doctor experienced the worst nightmare yet. Those guards - so many of them for one sick girl - how they abused Rhea! How they touched her, and starved her. How they would draw cuts into her skin as they held her down and re-do them after she had regenerated. How they talked of her people and family. The way they called out the names her children and laugh as she cried for her savior.

Before the Doctor knew it, he was sitting there crying. He just couldn't imagine what Rhea had gone trough, he knew. Now what little of her memory had been good was being eaten away. Now what little he can hold of her was scarred and beaten.

The Doctor whipped his eyes and stood up. He needed to be strong. He has lived too long without her to break down. He was the man and needed to be one, for her sake.

He checked her vital signs first. She was still just as bad as when he had left. Then he held her hand and closed his eyes. The parasite had slowed down a little bit, which was a great relief. But he was sure the virus was taking a break to cause even more damage later. He needed to act quickly if he wanted his wife back.

The Doctor walked behind her bed and stood over her, right above her face. Before he started to telepathically restore her health, he kissed her forehead for luck. Then placed his hands on her head, like he had done for Reinette and others in this past, and went through her head, all while humming an old Time Lord lullaby.

Suddenly, Rhea let out a small laugh. The Doctor stopped quickly. Rhea opened her eyes and looked straight above her, staring into the Doctor's eyes. She laughed more and looked away.

"You've always hated that song," she said quietly.

The Doctor sat in his chair again. "I did not and you know that."

"Oh, yes. You just banished it from the house, that's all."

The Doctor chuckled at the thought and knew she was right - like all wives. Then he asked, "How are you feeling?"

"Horrible. But your face helps millions."

"Rhea, please. No joking. Where does it hurt?"

"How am I joking? That new smirk of yours is enchanting."

"Rhea..."

"Fine. Everywhere, then. My head feels like it's being burned alive, but my temples feel like hammers are just having a field day."

"Then we'll talk later." He got up. "The virus is letting up and that's why you're coherent. I must take advantage."

"Haven't changed a bit, have you?" she quipped with a grin.

The Doctor sighed, but he really did find it funny. "You're as bad as Amy."

"She's the red-head?" There wasn't any humor in her voice now.

"Mmm-hmmm." The Doctor held Rhea head and was only playing a little bit of attention.

"She's pretty."

"Now, don't get that way. Not yet. When you're better, you can hound me on all my companions."

"There's more?"

"There _were_."

"And what do you mean by...'companion'?" Rhea gave him a raised eyebrow.

"As in 'friend,' but it sounds more official than 'traveling mate.'"

"'Mate'?!"

"As in 'friend,' Rhea! Calm down, you're making yourself upset."

Rhea her rolled eyes. Despite her health, she'll be damned if she's sick while that red-headed minx walks around all cuddly and friendly with her husband...who she figured out was alive after all only three hours ago, but still.

"Rhea," the Doctor interrupted, "think of something old."

"Why?"

"Just to check."

"Okay." And she did so.

"That's not funny."

Rhea chuckled. "Is so."

"Thinking of my mother's face is not funny!" He sounded like he was smiling despite himself.

"You said somethin' old!"

"Rhea, for a dying former prisoner, you're sense of humor remains fully intact, you know that?"

"Well, for an old man, you sure do like 'em young."

The Doctor's eyes flew open. She was in his head now. He let go of her and sat down again, wearing a disappointed expression. "You don't trust me."

"Of course not. I was dead to you until today. You expect me to believe that you've lived alone for nearly a thousand years, drifting along with only the TARDIS, until now? No. You were always too promiscuous for a Gallifreyan."

"Well, you've never had a problem with that, now sweetie?"

"A wife never does until her husband goes off with some tramp."

"At least I know you're personality is keepin' up. And, just so you know, I was alone for centuries. Maybe fifty, sixty years ago I acquired my first companions. So...ha!"

"So who's River?"

The Doctor clapped his hands together, showing her that this discussion was done. He walked back once more and began the process of restoration.

"Rhea, your head isn't going to fully fix itself," he explained. "I'll have to supply memories and energy in order for your immune system to build up again. After that, you'll be able to eradicate the parasite because I cannot do it myself."

"Will it hurt?" Rhea's voice had shrunk. She sounded as weak as she did earlier. The Doctor knew that he had to get this done _now_. The virus was starting up again. If not, she would never stand a chance.

"Not for you."

"It's going to hurt you?"

"Only a little."

Rhea tried to sit up, but she doubled over in pain. The Doctor helped up, but this time, slowly. "You can't! I won't let you!"

"How? You're regressing. Besides, you've been through more hurt and torture than I. I'm a big enough boy to take it."

"Will it work?"

"Of course." But he wasn't so sure. He has never done something like this. He has never seen something like this! But Rhea needed him. She needed her mad hatter. Almost as much as he needed his sweet, sweet girl.

The Doctor closed his eyes and went into her psyche. He poured his life's story into Rhea's mind, releasing centuries of hidden pain, hurt, and sadness that the formerly supposed Last of the Time Lord was born into, lives through, and will die because of.


	6. VI: Homecoming

**A/N: **Hey, it's official! We are going into the Doctor's past on Gallifrey! :D Here on out, the story will be in chronological order rather than jumping around with the first five chapters.

In other news, if you guys see anything that contradicts anything that the Doctor has said in the series, tell me! I want this to be as accurate as possible and since I just started series 4 yesterday, I'm lost. Also, if anyone can tell me if the Doctor's planet was already blown up in the first original series (with the 1st Doctor), thanks. 'Cause I'm sort of confused about that detail.

Lastly, please review! I'm dying to know if you guys like Rhea and now I want to see if the dicrection I'm heading in is good enough.

Time Lord forever,

~Ms. Unusual-in-Groovy-Ways

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**DISCLAIMER: I do NOT own Doctor Who or any references to the show or anything else. 'Cause if I did, I'd be killing more people off than Moffat.**

* * *

_**Penance**_

_**VI**_

_**Homecoming**_

* * *

Far from Earth and the Milky Way, even farther than that galaxy far, far away, deep into the constellation Kasterborous, lies a pinkish orange planet from the beginning of time itself.

Its name will soon be but mist in the wind; known, but unseen. Here but gone. It will only be spoken when questioning its very existence, as if doubting its presence will erase its influence. Children will talk of it like myths and fables. Stories of a powerful people who held the fabric of the universe within their hands, ruling over time and space with an iron fist and an open heart. Myths of time machines that traveled and roamed the world will fill our kids' dreams. A race of philosophers and scientists so clever, Aristotle was deaf and dumb when compared - these are the fragments that this oh so powerful race will leave behind.

That orange planet is named Gallifrey - or _was_ or _will be_. No one knows when it came to be. No one knows when it actually left. But all that is known of this fabulous planet is that it was beautiful.

* * *

It was an autumn morning. The air was cool and had a slight edge in it. It was quiet, but as the twin suns just began to rise in the east, the sounds of nature brewing awoke. Birds tweeted, crickets chirped in protest, and the branches rustles as the breeze flew gracefully. Speaking off branches, imagine your typical tree - tall, thick brown trunk, plume of leaves on top - but with silver leaves. These metallic sparkles glistened in the moonlight like the eyes of Artemis, but blazed in the early sunlight as if Apollo smiled down on all creation. An entire wood looked as if it were alive with shining flames that danced to the sound of the morning.

The sun moved along, beginning to greet the city next. The metropolis looked like a combination of ancient Greek villas and futuristic square housing. Everything was a clean white and minimalistic in style. It was crowded and grouped close like a Roman neighborhood, but the houses were square and had golden domes. Far ahead, sitting like a king, was a castle. It was taller than anything we humans could have made a thousand year ago, but looked like nothing the 21st century could produce. The only way to describe is that it looked like something out of _Star Wars_. It looked like the temple on Naboo and the buildings on Corasant had a child and it was the Gallifreyan Cruciform.

But the glorious scene was cut short by the sound of a whirlwind. The air roared almost angrily as the gentle breeze was replaced with gusts of hot wind. Animals ran, scared and frenzied, as they tried to find a hiding place from the emerging sphere in the middle of the silver-tinged forest. The city wasn't disturbed by the noise, however. Well, not yet.

The sphere was a warm silver color with gold baubles wrapped around it. It wasn't really big; maybe the height of a refrigerator but the width a doorway. At first glance it was a pretty contraption, but close up it looked like it was used for batting practice. It was dented and deformed and was caked in dirt. The sound of the engines creaked and groaned, as if protesting. As it fully appeared, it was sad excuse for a time machine.

The hatch opened with a moan and a hiss. Smoke bellowed out before of it passengers could even make their way out. After the haze cleared, however, a man stepped out less than gracefully, cursing and kicking the sphere like it was its fault.

The man was probably in his mid-twenties. He had shaggy greyish brown hair and warm green eyes. He had handsome features and a mischievous smile that warned fathers to keep their daughters as far away as possible. He was tall, maybe 5'10'', but far too skinny to be considered anything...[insert vulgar human phrase here that means "hot," but is too inappropriate for children]

"Lucius," a woman's voice called out, "kicking it won't help a bit."

A young lady of about eighteen emerged from the TARDIS with an amused smile and a baby on her hip.

The man named Lucius looked up from his hissy fit. "Can you fly this thing, Catherine?"

"Of course not," she laughed.

"Then let the master handle it."

She rolled her eyes. "At least help me with the bags before you upset it again."

"Fine," Lucius mockingly groaned. "But that wasn't my fault last time!"

"Yes, of course, sweetie. You just hit it with a club and it decided to leave us behind on my father's doorstep. But I know for a fact that it wasn't _your_ fault."

Lucius plafully stuck his tongue out at her. "At least it wasn't _my_ father's. Speaking of him, I gotta fix this before he sees it."

"Is that why we landed so far away?"

"Mmm-hmm. And there's also a small cottege that my uncle left me before he left to travel that is our new home. It's nice. Better than that fort my parents have."

"How far is it?" Catherine shifted her weight, careful not to disturb the sleeping baby on her hip.

"Not far from here. It's actually close to the city, so the market and family isn't too way out. There's also a lake for the little one."

Catherine looked at her sleeping child and smiled. To think that only nine months ago in human time she was a typical girl eighteenth century London! Now she had an alien husband who was eager to take her to his home planet and a beautiful baby boy. Of course, at times it was difficult to wrap her head around the notion that she birthed an alien's son who apparently wasn't exactly half-human, but as she looked at her child's sleeping face, she felt like life was perfect.

"Lucius?"

"Yeah?" he called as he got whatever they needed out of the TARDIS.

"Are you sure we cannot name him 'John'? I've always wanted my first son to named after my father."

"No can do, Cat." Lucius dropped her many bags of luggage on the ground. "He needs a proper Gallifreyan name if my parents are to not kill us."

"Can I call him 'John?'"

"Now, Cat, you're already babying him! Besides, he is named after your dad technically."

Catherine scoffed. "How so?"

"His name means 'Doctor!'"


	7. VII: The Send-Off

**A/N: **Now that you've met the Doctor's parents, it's time to meet him as a boy! This chapter takes place years later when he is 8 years old. As for Rhea, she'll come into the story in about two or three chapters, maybe. Also, **_warning_**: I have given the Doctor a _**full name**_, but I'm not going to use it just yet. His name won't appear in dialogue and in the narrative, I'll refer to him as "the Doctor" or "young Doctor".

In other news, shout-out to **liz-king97** for being such a loyal reader! :D This chapter is especially for you and I hope you enjoy it immensely.

R&R,

~Ms. Unusual-in-Groovy-Ways

P.S. I forgot! Throughout these flashbacks, please imagine a young David Tennant (10th Doctor) through the years. For some reason, I cannot picture Matt Smith any younger than he already looks, so remember: David Tennant! I'll tell you when it is okay to picture the 11th Doctor again.

* * *

**DISCLAIMER: I do NOT own Doctor Who or any references to the show or anything else. 'Cause if I did, I'd be killing more people off than Moffat.**

* * *

_**Penance**_

_**VII**_

_**The Send-Off**_

* * *

Lucius Borealis and his wife Catherine Smith met in eighteenth century London. Catherine was a physician's daughter, but _her_ mother was the daughter of an English lord, so the small family of three socialized with members of society. Also, Cat's father, John, was a well-respected doctor and everyone in his profession looked to him as an inovator. But he had one flaw:

He had no sons.

A doctor's dream was to have at least one son intelligent enough to teach. With God's will, a father hoped that his offspring would be a man of medicine as well as his old man, if not better. But John, not matter how much he tried, was given only a girl.

That didn't stop him though. John, with nothing else to do, taught Catherine all he could about medicine. Day and night, her father would have her read thick, hard-covered books that made the King James Bible look like a pamphlet. Because of her extensive education, Catherine knew all two hundred six bones in the body, all the muscles and their types, and could diagnose almost every known disease in less than an hour. Her father was a proud man; but with arrogance, but with genuine pride of the knowledge that his baby girl could kick some serious man ass when it came to medicine. (Her father had a tendency to get a little ghetto too, if ya couldn't tell.)

Catherine, with all her heart and mind, wanted to be a nurse. She wanted to help the poor and cure them off their illnesses. She knew that being a doctor would be impossible, but her soul told her that she had to help her countrymen in any way, shape, or form.

Mama wasn't having that.

Being a nurse in the late 1700s was an ugly job, to say the least. Only poor women and prostitutes were nurses because they were desposible. No respectable, honorable lady would even dare consider such a profession. In fact, it was not even thought of as an honest job! It was a low position, reserved for the lowest of creatures. And Catherine's mother, Lady Cassandra, would not have her daughter - her young, _pretty_ daughter - destroy her life by being associated with such impropriety. Her daughter was to marry and marry well. She would not have any less.

And Catherine wouldn't either. On the even of her eighteenth birthday, she snuck out and ran away, not before leaving her father a note saying good-bye. By herself at such a young age, she went into the gutters of London and applied as a nurse. At first, the coordinators were shocked and refused. They said it themselves, no lady was to mingle with the common woman. But Catherine refused to leave and was eventually a nurse.

For months, she helped her fellow women and their children. She didn't care about their position or status. It didn't matter what they did or how they survived. She only worried about their health and whether or not they bore healthy, happy children.

One night, however, Catherine left in the middle of the night to fetch something from the market for one of her younger patients. It was late and dark and dangerous. The streets were quiet, but every so often a shadow moved. Suddenly, she was lost. In London. Alone. And she was pretty. She was in a dangerous position already, but she just dug her own grave.

Out of the corner suddenly, a man of about ten feet ran towards her. She didn't scream or runaway. She froze while her eyes grew to the size of the full moons. Despite being Protestant, she crossed herself and waited for death warmly.

That was when she saw him.

To put it quickly, Lucius blasted the ten foot beast thing (it was his science experiment that went horribly wrong) with a sonic gun. The black goo that exploded coated them both. Lucius laughed gayly, but Catherine's rebuttal was a hysterical hiccup/sob. He tried to comfort her, but she then started to beat him with an umbrella.

About five minutes later, Lucius managed to convince that he meant no harm and that, as an apology, he'd take her to dinner.

Catherine continued to hit him with the umbrella-turned-bat for insinuating that she was not a lady.

In summary, after a night of pursuing and hitting, Lucius had managed to impress her by asking her what she did. No man asked a woman that question! Before she hit, she said she was a nurse. They spent the night talking about medicine and mothers. Somehow he invited her to the TARDIS (disguised as a buggy) and he took her to the year 2000 and showed her modern medicine.

They married about three days later and within probably a month she was pregnant.

A little more than seven years later, their son, who had a messed up Gallifreyan name by his mom's standards, was a pleasant combination of his both parents' weird. He had his father's cheekiness and lack of care for other people's property. He looked like his dad, too. He had his grey-brown hair (only it was spiky), his endearing-yet-troublesome smile, and his skinniness. He didn't look like his mom very much (he wasn't ginger) but he had her eyes. Those warm, chestnut eyes...

The Doctor as a child was a happy one, like any other. Living in nature, he loved exploring and pretending. Because Catherine insisted on raising him half-human, she read him her favorite nursery rhymes and adventure stories. The Doctor's favorites were the _Chronicles of Narnia_ and _Treasure Island_. He loved the idea of talking lions and ruthless pirates. He loved the dazzling magic and fantastic heroes. Mostly by himself because the parents of his friends didn't like his human mom, the child Doctor played gladly, fighting off the evil and rescuing the innocent.

The Doctor didn't mind being an only child, but his parents did. See, on Gallifrey, parenting was considered a job. Please know, Gallifreyans could not have children the way humans traditionally do. Instead, when Time Lord are of age (30), a selected group from the same family has part of their DNA taken and these samples are mechanically put together to get children called cousins. Which ever kids have the greater percent of a couple's genes, those are given to that family. This allows some parents to have as many as 5 kids in one batch while others may get one.

Gallifreyan parents raise their children themselves for eight years, then the government takes the children and enrolls them into The Academy, where that learn to be true Time Lords.

The Doctor, unlike other Time Lords, was born. Despite his mother's species, he is hundred percent Gallifreyan, but that doesn't mean he is accepted. To have children so young by such a barbaric means was considered disrespectful to the Elders of the planet. The Doctor's parents tried to go to Earth several times and raise him as normal kid, but the Seven Elders wouldn't have it. He was a Time Lord and he would be raised by Time Lords...goddammit!

Catherine hated all of it. She hated the fact that her son was cast off as a freak, but would be forced to leave his parents to go to some school that didn't like him. She would watch her son play and dread the day he had to go to the place that would break his spirit.

And today is the day.


	8. VIII: Bad Wolf

**A/N: **Hello again and welcome back! This chapter, I think, was kind of long at first because it this plus the next chapter. To spare my one real reader (you know who you are!), I shortened it. The next chapter with feature that cursed Time Vortex and everyone favorite intergalactic psychopath as an equally psychotic child, the Master! :D

Once again please read and review. I'm never sure that I'm doing a good job, so if you like: review. If you don't: tell me why and still review.

Live long,

~Ms. Unusual-in-Groovy-Ways

* * *

**DISCLAIMER: I do NOT own Doctor Who or any references to the show or anything else. 'Cause if I did, I'd be killing more people off than Moffat.**

* * *

_**Penance**_

_**VIII**_

_**Bad Wolf**_

* * *

Once upon a midnight dreary...the Doctor was tucked into bed and snuggled his ratty, bow-tie-wearing teddy bear George for dear life. He was fast asleep, like any eight year old, dreaming peacefully.

Unfortunately, his parents did not have that pleasure. No matter what they did, they couldn't sleep. Their eyes wouldn't collapse under the weight of tiredness nor would their minds calm and turn off. They just started at the ceiling miserably, listening to the rustling of wind and the ticking of that old grandfather clock. They counted down in their heads and as the clock rung for twelve o'clock, Catherine couldn't help but release a strangled yelp.

It was time.

Lucius shot up and held his wife. He tried to comfort her, to soothe of her qualms, but she just cried softly into his shoulder. Her body shook ever so lightly under his arms as she sobbed. Despite what he could do to calm her, his efforts were fruitless. All of them were.

She wouldn't let him leave, she said angrily! She would not let them take her son away from her. She wouldn't allow them to take him to some godforsaken place where they'll just break his spirit. They'll change him and tell him that all his dreams and fantasies were wrong. They'll take her baby boy and crush him. She wouldn't have that. She just wouldn't!

But she was human. Time Lords were ever fascinated by our natural inclination to investigate and learn, but we were a level five planet. We were backwards at best. For a Gallifreyan to be raised by mother who didn't understand half of her own galaxy was a preposterous statement. Her species was all the more reason to take her son away and raise him correctly.

Lucius abandoned all hope for his wife. She would calm down when her time came. So he got out of bed and forced himself to get ready for the tradition. Since he wasn't even close to being an adult Time Lord (he was only 32), he dressed in traditional student uniform. It was sort of like the elaborate Time Lord costume, but much shorter and without that stupid collar. It resembled a Roman soldier's battle armor, minus the exaggerated plume.

As he dressed, Catherine tried to control her breathing. She wouldn't see her son for years (she couldn't participate in the ritual because of her birth), so she had to make the most of her last moments with him. She got up and cleaned up, putting on her best happy face for her child.

Catherine tip-toed slowly into the room. She couldn't help but smile at the sight of the Doctor sleeping his face. He looked so serene, not a care in the world. Oh, how Catherine wished that were true. How she wished...

She sat on the edge of his bed, and called his name out. He stirred before he sat up. He rubbed his eyes and looked incredulously at his mom, like waking him up was such a confusing thing to do.

"Mom, it's not morning," he grumbled.

"Yes, it is," she whispered. "It's just that the suns are still sleeping."

"It's dark. I want to go back to sleep."

"Oh no you don't!" she said as she tickled him. He giggled and swatted his mom away playfully. "It's time to go now, sweetie."

"But I don't want to. I wanna spend my birthday here, with you and Papa."

Catherine tried to act like she happy for him to go to school and convince him that it was fun. But the Doctor, even as a child, was not going to believe something like that. Like his hero once said, he had a bad feeling about this...

"But, honey, it is such a nice place! You can go learn, play, and make friends. Isn't that nice?"

"No, Mama," he mumbled sadly. "I've had bad dreams about that place. I don't wanna go."

"Sweetie, it is not for you to decide. You have to go to school with all the other children."

The Doctor hung his head. In truth, he didn't like other children. They made fun of him and pushed him around. He liked his Mama and Papa better. He liked playing and reading by himself. The other children just called him names and ignored any time he wanted to play with them. He didn't want to go to a place where he would be alone and away from his Mummy and Daddy.

"Go get dressed," Catherine ordered. "I'll check on Daddy."

Lucius was already outside the house, standing at attention in front of the door. He was to wait for the Elder of Arcadia and great him before he handed over his son to the Academy. Lucius turned his head and saw his wife looking at him through the window. He smiled, to reassure her that is was a good thing. His son didn't have to be alone anymore...

As the family of three prepared themselves, the quiet night broke at the sound of footsteps. Well, not footsteps, but marching ones, like an entire battalion was striding into war. It was the Elder and his Escorts. The old man with grey-white hair was dressed in a traditional Time Lord get-up (red spandex-y robe and all). He carried a gold scepter with silver vines that intertwined around the handle. The sphere on top was diamond the size of a baseball and was laced with vines as well. The Elder held in vertically in his left hand as he possessed an old, rugged book in the other. He was followed by about fifty other men, all young and handsome, dressed in the same outfit as Lucius. Gallifreyans, if not traditional, were a grand people nonetheless.

Catherine's heart stopped at such a sight. All these people, for one boy?! She could not believe her eyes, but she knew she didn't have time to stand around and shake her fist at the sky. This was her last moment with her son. The last one she will get for years. She had to make the most of her, for her sake and, most importantly, the sake of her baby boy.

The Doctor hobbled out of his room, with a sad face only a boy can make. He made his way to his mom and fell into her arms. She grasped her son and held him for dear life. She could hear her husband talking with the Elder. It was time. No more waiting. No more sleepless nights awake worrying over how many days she had left. It was over. It was all over.

Cat broke the hug and peered into her son's eyes. He had her eyes, God bless him, she thought. She gently cupped his cheek and stared into those warm orbs that she had to see everyday of her life. Without words, but with tears, she smiled her good-bye. The Doctor, even as a boy, knew that was as much as the situation would give him. He understood that his mother would not be abled to vocalize her farewells for how was a mother supposed to officialize such an event? To expect a caretaker to personally terminate a relationship _with her own son_ was ludicrous at best.

Lucius pranced into the small, simple living room to witness the silent adieu. He painfully smiled as his son ran up to him. He lifted him up like a mere bag of socks and hefted him onto his shoulders. He wouldn't cry himself, in front of his family, but on the inside, the father's hearts ached unmercifully. One for his wife's grief, the other for his only (leaving eight-year-old) son.

Catherine stood up and kissed her husband before she did the same to her boy. In her grandmother's native French, she wished her son a safe and happy journey and promised him that they'll see their little man_ very_ soon. This shocked Lucius because all he could muster was a grin. After this, Catherine watched as her two men strutted out the front door, wishing she could damn her human nature and give her baby a proper send-off.

* * *

Gallifrey was a world as old as time and as wise as his wife. Before any other species could walk, Gallifrey was a land of culture and knowledge. They built a nation of democracy and tradition while humans and our cousins were trying to make a fire out of twigs and stones.

Gallifrey was a partial monarchy. It was divided into seven cities: one each in the north, east, west, north-east, north-west, south-east, and south-west (never the south, for it was bad luck). Between them, there were the Woods, a sort of no-man's-land where the people could retire and socialize. Each city was ruled by an Elder. The largest city with the most powerful and respected leader was Arcadia in the north. It was center of learning and culture in the whole planet. This was the place where government happened and where the Academy was located.

The Academy was a beautiful, ancient castle located at the side of the highest mountain, Mount Gaea*. To the west of the mountain, fields of glowing red grasses stretched as far the eye could even imagine to see. In the spring, nothing was more breath-taking than watching the sunsets erupt the sparse silver trees and ignite the shining plains, illuminating the world as if it were a burning flame. To the east, a steep cliff about a three miles deep led to the Gold Sea, named after the color it turned into when the suns were out.

The castle itself was the most marvelous sight we humans could even see. Like ours, it was enormous, with spires and towers and walls and bridges connecting to all those massive rooms. It was sort of like Hogwarts in architecture, but what Godric Gryffindor would give to have this place. It was made out of pure white marble, making it glisten like an angel within the deep banks fiery Hades. Its roof tops were all sorts of metal, most of them not yet discovered on Earth. Its gates were platinum, with a crest the size of door, depicting a red hourglass in equal halves.

The Academy was a boarding school, where Time Lord children, at the tender age of eight, would learn all about their history as well of the universe's. From day one, they are trained to understand the incomprehensible concept of time, how to manipulate it, and how to respect. They taught the customs of their people as well the ones of others. By the age of eighteen, the children graduate and go to the Gallifreyan version of college where they learn a specific profession that they will use throughout their infinite lifetime.

Today, the Doctor and several other children will be inducted to the school.

The Elder rarely ever enrolled a child personally (he would send his next-in-commands to do so), but the Doctor was an anomaly. He was the spawn of Time Lord and human, but was predominately Gallifreyan. That should never happen under any circumstances. It contradicted everything Gallifreyans are taught! But this child - this _boy_ - lived and was ever so Time Lord. The Elder had to personally enroll him and see what the universe had in store for this oddity.

Elder Rassilon watched curiously as Lucius approached him, with the child on his shoulders. He looked just like his father, with his toothy grin and wild hair that never seemed to stay down. He looked Time Lord...enough.

"Bring the boy forward," Rassilon commanded in a loud voice.

Lucius put his son down and scooted him toward the old dude.

"His given name, soldier,"

Lucius announced his son's messed up name to the group of men. If they weren't soldiers, they would of laughed at what a ridiculous mixture of Old High Gallifreyan and English. To not give anything away (the Doctor is always watching, I suppose), let's say it was Gallifreyan, the English equalavant of that Gallifreyan word, a human name, a Latin/Greek last name, and another last that rhymes with "crystal meth" (or was it "myth?").

Rassilon only response was a raised eyebrow that really meant "Really? WTF, you really named him that?" Instead of dragging the subject any further, he opened the large, worn book. After finding whatever he needed to find (this act requires a complicated process of taking the initials of that children, translating them to Gallifreyan, and finding it in that big book), the Elder beckoned the Doctor over and anointed him with the scepter, all while saying something in that oddly beautiful language that sounds like a whirlpool singing a nightingale's melancholy song.

In English it would translate:

"By the authority of the Universe and the guidedance of the Galaxies, I rename you in the honor of Time, my Lupus Malus."

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_*Gaea (pronounced **GAY-ah**), Greek mother/personification of the earth, wife of the sky god, Uranus_


	9. IX: The Vortex

**A/N: **Sorry for the delay! I accidentally wrote over this chapter (don't ask why or how), so I had to re-write everything. However, this draft, I think, is far better than the first and makes more sense. Also, if you didn't read the last time, the Master appears for the first time in this chapter as a young boy! :D

Something I want to say too, is that in _The Journey's End_, the last episode of series 4, the Doctor says he visited the Mudusa Cascade when he was just a boy - 90 years old. I'm choosing to ignore this by saying this: this is relative. To Time Lords, anything under 300 is young. Also, with what I'm making up, Time Lords have years of schooling in many different times of their long lives. Just wanted to clear this up 'cause as I continue to learn more about the Doctor, it's just more I gotta deal with.

Gotta go now, so buh-bye,

~Ms. Unusual-in-Groovy-Ways

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**DISCLAIMER: I do NOT own Doctor Who or any references to the show or anything else. 'Cause if I did, I'd be killing more people off than Moffat.**

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_**Penance**_

_**IX**_

_**The Vortex**_

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The Doctor was immediately instructed to walk with the Elder and leave. Without even looking back, he left his home far behind him. He desperately wanted to turn around and run into his Daddy's arms where he'd take him inside and have his Mummy hug him until the tears stopped. But he couldn't. The soldiers around him kept telling him to march along the narrow road that led into the city.

As the massive entourage entered Arcadia, the young boy saw such a sight. Fathers all dressed in their traditional battle uniform were standing outside their doors with their children. Something were completely stoic, looking ahead emotionlessly as their kids cried and whimpered. But there were some that, despite their hardened demeanor, couldn't completely mask their pain. In their eyes, the Doctor saw a sadness he knew his Mummy had felt just minutes earlier. It was a difficult sight to explain, but just imagine when your a father in the near/far future and you're forced to hand over your child. How would you feel? What ache in chest would destroy your composure?

All the children filed behind the Doctor. Some of them were like their fathers: countenance maintained, expressions blank. Then they were children who weren't soldiers. They cried hysterically. A few of them ran back to houses, where sobbing mothers couldn't help but embrace their babies. It was a horrible sight to watch, but the Doctor, even as a boy, couldn't look away from this so called tradition. He stared intently as he marched at the fathers carrying their kids back to the line, half angry, half still trying to keep themselves from crying.

After what seemed like forever-and-a-half, the large group of soldiers/children walked along the worn out path led by the Elder Rassilon. He acted like he hadn't even noticed all the tears. He just walked forward, ignoring the still screaming kids. He was somewhat like a shark, swimming forward to forget what could kill him.

The path was not any better than a dirt road. Despite the fact that it was a sacred road that led to the holiness place in the universe, it was just a sad dirt road. Only simple torches on the sides lit the way. But it was not any ceremonial torches plated in gold and silver and encrusted with deep, colored jewels or mother-of-pearls. Just torches. As good as a torch can realistically get.

Anyway, the Holy Backwoods Road curved through the northern part of the Woods. It led deep into the trees, so deep that the two moons' light couldn't even shine through the black canopy over head. The battalion walked ahead stoically, but the children shivered in fright. The trees, the farther they walked, became more gnarly and knotted. The branches were unruly and continually slapped them and tripped them over. The green of the forest was drowned out by the overwhelming presence of inky black that seemed to move, suffocating all the light in its dead wood.

The trees cleared slightly to show a rocky ledge that turned into Mount Gaea. It was a narrow street made out of rocks that have probably been their since the first Time Lords. Only two people at a time could pass. The Doctor was the first children to follow the Elder across. He was terrified. His mom didn't like heights. She would even climbs tree or the TARDIS with Lucius or her son. The Doctor never understood why she was so scared of being off the ground. But as he looked down, he saw the trees shrinking and the city walk away from his eyes. Vertigo caught him, but the centurion he was paired with took his hand and pulled him forward. In a nice way too, that made the Doctor very grateful.

At the very top of the mountain was the school, but Rassilon took a detour. Instead of following the rocky path that spiraled up the side of the mount, Rassilon found yet another sad, sad dirt road. The kids started to mumble in protest and question the old guy's judgement, but they still marched along the totally dark runway until they heard a gravely voice shout, "STOP."

They did as they were told. They waited impatiently but soon torches were lighted in a fit of flames. They were lit in order until it hit a group of men far away from them. They were about six of them, all dressed like Rassilon. The were formed in a semi-circle, in front of something. They couldn't exactly make it out, but it seemed to glow and hum, like it was alive.

The centurions bowed and marched back down the mountain. They left the children alone with the Seven Elders of Gallifrey as they were ordered to do. But that didn't mean they wanted to. They knew what would happen next. The children would be forced, one-by-one, to look into the Vortex of Time. They would stare at time itself and the whole of infinity. It was a marvelous sight and grabbed on to you like it needed you to bask in its glorious beauty. But what followed hurt. Some children would be inspired, others would run away in fear, but some - some would go insane, such a sight burning itself into their minds like a hot brand. Staring into the heart of time was like looking into the belly of the beast...it changes you.

They children were ordered to stand at attention, with their backs facing the Vortex. They were close enough to hear, but not enough to understand what was going to happen. Gallifreyans thought that this part brought out a child's character even before they were tested. But if you heard another kid scream in terror wouldn't you break down crying? But this logic escaped the Time Lords. Surprise, surprise...

A child's name was called in Gallifreyan. The boy turned with sad blue eyes and faced the Elders, trying to be brave. But he was a small boy, he looked like he was a skinny five-year-old rather than an eight-year-old. But he as he walked away from the other kids, he puffed out his chest and marched.

To his damnation.

The Elder of Arcadia guided him up to the vortex slowly, telling him to let his soul see rather than his eyes. He faced it and looked and died inside instantly.

What he saw that day could never be told in actual words, but it was war, to be simple. Some say it was the Time War. Others say it was the war inside him being told through gory, broken images. Maybe it was every war that has ever ravaged universe with their stupidity. But no one is certain. But what little the Master has said reveals that there was blood. Seas of it. People swimming lifelessly atop the red goo. People bleeding like waterfalls, their wounds gushing that thick liquid. Blood - just everywhere. Being drunk. Bathed in. Just blood. The redness piercing every color. Drowning anything - literally.

The Master's scream erupted the night. It sounded like a blade cutting the silent in halves. He fell to his knees, but didn't stop screaming. He yelled louder and louder and didn't stop. He _couldn't_ stop. He just yelled as loud as a boy's lungs could muster...multiplied by infinity. His shrieks tore the night and made it bleed. That's why he screamed. He saw death and carnage and brutality and everything was red and screaming in it. He yelled for his vision. His vision would be heard and it was. The high-pitched roars mixed with gurgled sobs was heard and echoed through the forests like wailing ghosts.

Wailing, wandering ghosts clothed in the red pain of a child's life ruined.

Now it was the Doctor's turn! ;D

The Doctor's face was covered in wet tears and he started to protest as the Elders ordered him to come. He shook their hands off as he saw them cart a still yelling Master away from him. He couldn't let this happen. He cried, kicked, and screamed. He wouldn't look. He would not stare in whatever made that kid die and come back as a banshee. He couldn't lose like this. He wouldn't look. HE WOULDN'T LOOK.

But the Elders held him down. They threw him on his knees and held his face to the Hole in Space. They made him open his eyes and what he saw he never said. Unlike the Master who desperately had tried to vocalize that night's vision, the Doctor never opened his mouth. He just said he ran. And that's true. He did run - like if he was the Flash who needed to pee **_now_**. But he never said how he fell over his feet and instead of getting up to run some more, he turned around and looked at into the Vortex. In his face still red and puffy and wet, he stared into Time and Space and he smiled. What he saw that made him smile...*shruggs*...I don't know. But the Elders were shocked as they witnessed the crying boy waving into Time. They stood flabbergasted as the Doctor laughed and wiped away a stray tear. He waved his good-bye one last time and ran once more.

And he's never stopped.


	10. Interlude: Rupture

**DISCLAIMER: I do NOT own Doctor Who or any references to the show or anything else. 'Cause if I did, I'd be killing more people off than Moffat.**

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_**Penance**_

_**Interlude**_

_**Rupture**_

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Amy woke up slowly. Her sleep had been the image of peaceful. She opened her eyes to see her husband's sleeping face, still frozen in a state of bliss. With her eyes, she traced his face. She knew it by heart by now, but she loved to just look and count the birthmarks, the eyelashes. She looked at his silent expression and sighed quietly. _What a face..._

She got up from bed and readied herself. Dressing in an oversized sweater and jeans, she left her Converse behind so she could make breakfast for her boys.

_Her boys..._

She ran out outside, to see if it was just a dream. _Please, oh please! Let him be okay..._

The TARDIS was empty. Not even a hum showed life. She checked the lower levels of the control room to see if he was there. She'd raced down for nothing. She had tripped down for nothing. The Doctor wasn't there at all.

So it was true.

_She _was_ here..._

With a soft yelp, she collasped onto the floor. She held her knees close to her chest and tried in vain to control her sobs. But they echoed off the walls, infinately replaying her sadness.

_He wasn't okay. He would never be okay again..._

She desperatey tried to wipe away the tears, end the hot droplets from falling. But she couldn't stop crying.

Not anymore.

Not ever again.

_Not after Rhea..._


End file.
